A £13bn overhaul of the NHS records system has suffered so many problems that hospitals have struggled to keep track of people requiring operations, patients with suspected MRSA and potential cancer sufferers needing urgent consultations.

Glitches in the roll-out of the Connecting for Health computer system have also resulted in delays at accident and emergency departments, soaring complaints and failures to identify child-abuse victims.

The revelations are just the latest setback for what the government has pledged will be a key factor in improving NHS services. According to the board minutes of the first London NHS trusts to install the new system, obtained by The Observer and Computer Weekly, it has had a serious effect on patient care, a problem that raises questions about its introduction to hundreds of other hospitals and trusts.

A report to the Enfield Primary Care Trust in March reveals that difficulties with the system last year meant it did not have vital data identifying patients awaiting operations. As a result 63 patients of the Barnet and Chase Farm Hospitals NHS trust had their operations delayed.

In April, the trust found that the system had failed to flag up possible child-abuse victims entering hospital to key staff, 'leaving the responsibility to the receptionist'.

The same trust noted the following month that 272 elective operations were cancelled at the last minute for 'non-clinical reasons' and that 20 patients were not readmitted for treatment within 28 days at the end of last year because the 'surveillance system for tracking' them 'was not operational in the new ... system'.

The board's minutes show 14,000 people contacted the trust last year with concerns about their treatment, compared with 5,500 in 2006.

A report to the board of another NHS trust, Barts and the London, says that for six months to May this year the trust failed to meet targets for treating emergency patients within four hours, chiefly because staff were unfamiliar with the new computer system. The same report reveals that in May there were 'breaches of the two-week urgent cancer access guarantee' for the same reasons. As a result 11 patients who were suspected of having cancer did not receive consultations on time.

According to minutes presented to the Buckinghamshire Hospitals NHS Trust, problems with the new system last year meant potentially infectious patients with MRSA were not isolated for up to 17 days. The problem had to be rectified manually by staff who updated the patient records themselves. 'This took approximately six weeks to do, during which time there was a possibility that some MRSA-positive patients may have slipped through undetected if medical notes had not been available,' according to the report.

The revelations have prompted claims that the government is losing control of the flagship project. 'IT projects well implemented can be a huge benefit,' said Stephen O'Brien, the Conservatives' health spokesman. 'Clearly from the problems being encountered by many trusts, the benefits are not being achieved and all the risks are falling on patients.'

Many trusts have delayed implementing the new system as a result of the problems and the chief executive of Connecting for Health, Richard Granger, resigned last year. Those trusts that have implemented the system complain it diverts staff from key duties. A report last month to the board of the Royal Free Hampstead NHS Trust said 12,000 patient records had to be manually amended over a three-week period.

'The outpatient appointment centre has experienced a significant increase in the time taken to process individual patient appointment bookings. This has had a consequent and negative effect on call-answer performance,' the report states. The trusts said the problems had been or were being fixed. 'We are aware that during initials stages of implementation there were some difficulties,' said a spokesman for NHS London.

A spokeswoman for Connecting for Health said patients would be better off under the new system. 'Patients can expect faster diagnosis and treatment because vital information will be available wherever and whenever care is required.'